Dear users
I tried to run a MD simulation in parallel but the output file looked not good.
The input file to run the parrallel MD was (5ns in total):
#!/bin/bash -l
#$ -N PknGAde_md
#$ -l membycore=1G
#$ -l runtime=25:00:00
#$ -pe ompi 32
#$ -cwd
##$ -o $HOME/queue/stdout
##$ -e $HOME/queue/stderr
module load OpenMPI
#echo "Got $NSLOTS processors."
mpirun -v -np $NSLOTS pmemd -O -i PknGAde_md.in -o PknGAde_md01.out -p ../PknGAde_params/PknGHAdeH_ion_wt.prmtop -c PknGAde_equil.rst -r PknGAde_md01.rst -x PknGAde_md01.mdcrd
mpirun -v -np $NSLOTS pmemd -O -i PknGAde_md.in -o PknGAde_md02.out -p ../PknGAde_params/PknGHAdeH_ion_wt.prmtop -c PknGAde_md01.rst -r PknGAde_md02.rst -x PknGAde_md02.mdcrd
mpirun -v -np $NSLOTS pmemd -O -i PknGAde_md.in -o PknGAde_md03.out -p ../PknGAde_params/PknGHAdeH_ion_wt.prmtop -c PknGAde_md02.rst -r PknGAde_md03.rst -x PknGAde_md03.mdcrd
mpirun -v -np $NSLOTS pmemd -O -i PknGAde_md.in -o PknGAde_md04.out -p ../PknGAde_params/PknGHAdeH_ion_wt.prmtop -c PknGAde_md03.rst -r PknGAde_md04.rst -x PknGAde_md04.mdcrd
mpirun -v -np $NSLOTS pmemd -O -i PknGAde_md.in -o PknGAde_md05.out -p ../PknGAde_params/PknGHAdeH_ion_wt.prmtop -c PknGAde_md04.rst -r PknGAde_md05.rst -x PknGAde_md05.mdcrd
mpirun -v -np $NSLOTS pmemd -O -i PknGAde_md.in -o PknGAde_md06.out -p ../PknGAde_params/PknGHAdeH_ion_wt.prmtop -c PknGAde_md05.rst -r PknGAde_md06.rst -x PknGAde_md06.mdcrd
mpirun -v -np $NSLOTS pmemd -O -i PknGAde_md.in -o PknGAde_md07.out -p ../PknGAde_params/PknGHAdeH_ion_wt.prmtop -c PknGAde_md06.rst -r PknGAde_md07.rst -x PknGAde_md07.mdcrd
mpirun -v -np $NSLOTS pmemd -O -i PknGAde_md.in -o PknGAde_md08.out -p ../PknGAde_params/PknGHAdeH_ion_wt.prmtop -c PknGAde_md07.rst -r PknGAde_md08.rst -x PknGAde_md08.mdcrd
mpirun -v -np $NSLOTS pmemd -O -i PknGAde_md.in -o PknGAde_md09.out -p ../PknGAde_params/PknGHAdeH_ion_wt.prmtop -c PknGAde_md08.rst -r PknGAde_md09.rst -x PknGAde_md09.mdcrd
mpirun -v -np $NSLOTS pmemd -O -i PknGAde_md.in -o PknGAde_md10.out -p ../PknGAde_params/PknGHAdeH_ion_wt.prmtop -c PknGAde_md09.rst -r PknGAde_md10.rst -x PknGAde_md10.mdcrd
After a little while this is the output file I got:
NSTEP = 0 TIME(PS) = 505.000 TEMP(K) = 302.59 PRESS = 29.9
Etot = -68586.9701 EKtot = 17670.5627 EPtot = -86257.5328
BOND = 733.9414 ANGLE = 2020.1809 DIHED = 2561.7581
1-4 NB = 886.3579 1-4 EEL = 8826.9539 VDWAALS = 9336.8900
EELEC = -110623.6151 EHBOND = 0.0000 RESTRAINT = 0.0000
EKCMT = 7379.8023 VIRIAL = 7197.1536 VOLUME = 282916.5283
Density = 1.0267
Ewald error estimate: 0.1600E-04
------------------------------------------------------------------------------
NSTEP = 500 TIME(PS) = 506.000 TEMP(K) = 297.82 PRESS = 184.9
Etot = -68782.7766 EKtot = 17392.3877 EPtot = -86175.1643
BOND = 760.3712 ANGLE = 2018.3147 DIHED = 2577.6310
1-4 NB = 868.4552 1-4 EEL = 8848.8665 VDWAALS = 9469.6912
EELEC = -110718.4941 EHBOND = 0.0000 RESTRAINT = 0.0000
EKCMT = 7211.7000 VIRIAL = 6081.0981 VOLUME = 283223.4172
Density = 1.0256
Ewald error estimate: 0.7075E-04
------------------------------------------------------------------------------
NSTEP = 1000 TIME(PS) = 507.000 TEMP(K) = 303.38 PRESS = -32.1
Etot = -68535.9124 EKtot = 17717.1269 EPtot = -86253.0393
BOND = 744.5244 ANGLE = 2050.0930 DIHED = 2611.1658
1-4 NB = 890.8984 1-4 EEL = 8814.2313 VDWAALS = 9474.0224
EELEC = -110837.9745 EHBOND = 0.0000 RESTRAINT = 0.0000
EKCMT = 7424.8877 VIRIAL = 7621.2398 VOLUME = 282951.8893
Density = 1.0265
Ewald error estimate: 0.1217E-03
------------------------------------------------------------------------------
NSTEP = 1000 TIME(PS) = 507.000 TEMP(K) = 303.19 PRESS = -100.8
Etot = -68320.4189 EKtot = 17705.7904 EPtot = -86026.2093
BOND = 773.9659 ANGLE = 2070.6064 DIHED = 2562.0428
1-4 NB = 895.2760 1-4 EEL = 8807.0426 VDWAALS = 9310.0092
EELEC = -110445.1521 EHBOND = 0.0000 RESTRAINT = 0.0000
EKCMT = 7513.8965 VIRIAL = 8128.6718 VOLUME = 282587.6144
Density = 1.0279
Ewald error estimate: 0.8968E-04
------------------------------------------------------------------------------
NSTEP = 1000 TIME(PS) = 507.000 TEMP(K) = 299.75 PRESS = -36.4
Etot = -68738.2193 EKtot = 17505.2526 EPtot = -86243.4719
BOND = 738.8328 ANGLE = 2031.7181 DIHED = 2553.6926
1-4 NB = 935.2209 1-4 EEL = 8825.3011 VDWAALS = 9141.6998
EELEC = -110469.9372 EHBOND = 0.0000 RESTRAINT = 0.0000
EKCMT = 7279.8267 VIRIAL = 7502.2703 VOLUME = 282788.2929
Density = 1.0271
Ewald error estimate: 0.6333E-04
------------------------------------------------------------------------------
NSTEP = 1000 TIME(PS) = 507.000 TEMP(K) = 298.25 PRESS = -3.4
Etot = -68906.5624 EKtot = 17417.1935 EPtot = -86323.7559
BOND = 730.0224 ANGLE = 2004.3585 DIHED = 2593.6427
1-4 NB = 915.7846 1-4 EEL = 8848.5493 VDWAALS = 9310.3188
EELEC = -110726.4322 EHBOND = 0.0000 RESTRAINT = 0.0000
EKCMT = 7395.6437 VIRIAL = 7416.6835 VOLUME = 282563.3958
Density = 1.0280
Ewald error estimate: 0.2572E-04
------------------------------------------------------------------------------
NSTEP = 3000 TIME(PS) = 511.000 TEMP(K) = 298.52 PRESS = -83.8
Etot = -69103.9397 EKtot = 17433.0164 EPtot = -86536.9561
BOND = 739.7540 ANGLE = 1911.9645 DIHED = 2559.3395
1-4 NB = 889.5156 1-4 EEL = 8837.7004 VDWAALS = 9191.4425
EELEC = -110666.6728 EHBOND = 0.0000 RESTRAINT = 0.0000
EKCMT = 7362.8144 VIRIAL = 7874.5779 VOLUME = 282776.7413
Density = 1.0272
Ewald error estimate: 0.1750E-04
------------------------------------------------------------------------------
NSTEP = 1500 TIME(PS) = 508.000 TEMP(K) = 299.03 PRESS = -170.3
Etot = -68919.6723 EKtot = 17462.8779 EPtot = -86382.5503
BOND = 792.4948 ANGLE = 2070.5043 DIHED = 2563.6783
1-4 NB = 862.9833 1-4 EEL = 8778.7242 VDWAALS = 9283.6592
EELEC = -110734.5943 EHBOND = 0.0000 RESTRAINT = 0.0000
EKCMT = 7272.0592 VIRIAL = 8310.6229 VOLUME = 282477.7558
Density = 1.0283
Ewald error estimate: 0.7074E-04
------------------------------------------------------------------------------
NSTEP = 1500 TIME(PS) = 508.000 TEMP(K) = 300.77 PRESS = -282.3
Etot = -68833.0371 EKtot = 17564.7690 EPtot = -86397.8061
BOND = 740.1230 ANGLE = 2032.8573 DIHED = 2589.5547
1-4 NB = 921.7805 1-4 EEL = 8819.1197 VDWAALS = 9396.2420
EELEC = -110897.4832 EHBOND = 0.0000 RESTRAINT = 0.0000
EKCMT = 7382.0096 VIRIAL = 9106.3200 VOLUME = 282884.6148
Density = 1.0268
Ewald error estimate: 0.1224E-04
------------------------------------------------------------------------------
NSTEP = 4000 TIME(PS) = 513.000 TEMP(K) = 298.93 PRESS = -41.7
Etot = -68704.6248 EKtot = 17457.1529 EPtot = -86161.7778
BOND = 746.9128 ANGLE = 2015.4375 DIHED = 2583.2619
1-4 NB = 898.4532 1-4 EEL = 8819.9182 VDWAALS = 9238.1231
EELEC = -110463.8845 EHBOND = 0.0000 RESTRAINT = 0.0000
EKCMT = 7323.6228 VIRIAL = 7577.9148 VOLUME = 282583.6933
Density = 1.0279
Ewald error estimate: 0.3978E-04
------------------------------------------------------------------------------
NSTEP = 5000 TIME(PS) = 515.000 TEMP(K) = 300.36 PRESS = -70.5
Etot = -69044.4020 EKtot = 17540.8579 EPtot = -86585.2599
BOND = 748.7331 ANGLE = 2017.1058 DIHED = 2530.9318
1-4 NB = 884.0729 1-4 EEL = 8785.5771 VDWAALS = 9653.3454
EELEC = -111205.0260 EHBOND = 0.0000 RESTRAINT = 0.0000
EKCMT = 7366.1062 VIRIAL = 7797.2388 VOLUME = 283410.8559
Density = 1.0249
Ewald error estimate: 0.1346E-03
------------------------------------------------------------------------------
Thus, something wrong append, but I do not know what. It is the first time i try to run MD in parallel.
Any suggestion?
Best,
Valentina
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Valentina Romano | PhD Student | Biozentrum, University of Basel & SIB Swiss Institute of Bioinformatics
Klingelbergstrasse 61 | CH-4056 Basel |
Phone: +41 61 267 15 80
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Received on Tue Jun 10 2014 - 08:30:02 PDT
